Kondo2014Nakamura

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JournalofMolecularCatalysisB:Enzymatic110(2014)23–31

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JournalofMolecularCatalysisB:

Enzymatic

journalhomepage:www.elsevier.com/locate/molcatb

AsignificantroleofArg41residueintheenzymaticreactionof

haloaciddehalogenasel-DEXYLstudiedbyQM/MMmethod

HirotakaKondoa,∗,TakashiNakamurab,ShigenoriTanakac,∗

aGraduateSchoolofHumanDevelopmentandEnvironment,KobeUniversity,3-11Tsurukabuto,Nada,Kobe657-8501,JapanbNagahamaInstituteofBio-ScienceandTechnology,1266Tamura,Nagahama,Shiga526-0829,JapancGraduateSchoolofSystemInformatics,KobeUniversity,1-1Rokkodai,Nada,Kobe657-8501,Japan

articleinfo

Articlehistory:Received7April2014Receivedinrevisedform23August2014Accepted12September2014Availableonline22September2014

Keywords:Enzymaticreaction2-Haloaciddehalogenasel-2-ChloropropionicacidONIOMmethodTransitionstateabstract

l-2-Haloaciddehalogenase(l-DEX)isoneofafamilyofenzymesthatdecomposeavarietyofenvi-ronmentalpollutantssuchasl-2-chloropropionate(l-2-CPA).Thisenzymespecificallyproducesad-2-hydroxyacidfromal-2-haloacid,and,todate,someresidueshavebeensuggestedasimportantinthisenzymaticreaction.Here,quantum-mechanical(QM)/molecular-mechanical(MM)calculationsforthel-DEXfromPseudomonassp.YL(l-DEXYL)2-CPAcomplexwereperformedtoelucidatethestruc-tureoftransitionstateandtheenergyprofileinthisenzymaticreaction.QM/MMsimulationsusingtheONIOM(PM3:Amber)methodrevealedthattheactivationenergyofdehalogenationreactionwasaround9.0kcal/molandthatoneofthemostimportantresiduesintheesterintermediateformationstepwasArg41,whichwasfoundtodecreasetheactivationenergybyabout40kcal/molcomparedtothecaseofitsabsence.Ontheotherhand,thisstabilizationeffectbyArg41wassignificantlycounterbalancedbythepresenceofAsn177.SimulationsofenzymesmutatedatArg41indicatedthatmutantspossessingapositivechargeneartheArg41positionwouldallowthedehalogenationreactionaswell.Specifically,itwassuggestedbyoursimulationsthathomolysine(homK)mutantofArg41,whichcontainsonemoremethylenegroupinthesidechaincomparedtolysine,couldbeactiveaswellasthewild-typeenzyme.Thedistancefromthechlorideiontothepositionofthepositivechargeoftheacceptorseemstodictatetheactivationenergy.©2014ElsevierB.V.Allrightsreserved.

1.Introduction

Manyorganohalogencompoundsareknowntobeproduced

biologicallyorbynaturalabiogenicprocesses[1].Producedin

largequantitiesbythechemicalindustryduetotheirusefulness

assolvents,pharmaceuticals,andagrochemicals,thesechemicals

alsocauseseriousenvironmentalpollutionandhealthproblems.

Dehalogenasesdetoxifyvarioushalogencompounds,catalyzing

theremovalofahalogenatomfromtheirsubstrates,andareuse-

fulinenvironmentaltechnologytodecontaminateenvironments

pollutedwithharmfulorganohalogencompounds.

2-Haloaciddehalogenaseshavebeenextensivelystudiedand

reviewed[2,3].Onedehalogenase,l-2-haloaciddehalogenase(l-

DEX),catalyzesthehydrolyticdehalogenationofl-2-haloalkanoic

acidstoproducethecorrespondingd-2-hydroxyalkanoicacids

∗Correspondingauthors.Tel.:+810788036620;fax:+810788036621.E-mailaddresses:kondo@eniac.scitec.kobe-u.ac.jp(H.Kondo),tnakamura@nagahama-i-bio.ac.jp(T.Nakamura),tanaka2@kobe-u.ac.jp(S.Tanaka).withthereleaseofhalideions.Arepresentativeenzymeofthe

haloaciddehalogenasesuperfamily,l-DEX,hasbeenisolatedand

purifiedfromseveralmicrobialstrains[4].l-DEXYLwasisolated

fromPseudomonassp.strainYLcellcultureinamediumcontaining

2-chloropropionate(2-CPA)asthesolecarbonsource[5].Thereac-

tionmechanismsofl-DEXYLhavebeenanalyzedbysite-directed

mutagenesis[6],X-raycrystallography[7–9],massspectrometry

[10–12],18O-incorporationexperiments[13],andcomputersimu-

lationsbythemoleculardynamicsandfragmentmolecularorbital

methods[14].

Site-directedmutagenesisexperimentshaverevealedthat

thoseaminoacidresiduessuchasAsp10,Thr14,Arg41,Ser118,

Lys151,Tyr157,Ser175,Asn177andAsp180areimportantforthe

catalyticfunctionofl-DEXYL[6].18O-incorporationexperiments

haverevealedthatAsp10playsapivotalroleinanucleophilic

attackonasubstrate˛-carbontoformanesterintermediate,

whichisthenhydrolyzedbywater[13].Thesestudiessuggestthe

reactionmechanismshowninFig.1.Massspectrometryanalysis

hasshowntheinvolvementofArg41andAsp180intheformation

ofanesterintermediate[12].X-raycrystallographicanalysisof

l-DEXYLhasprovidedfurtherevidencefortheformationofan

http://dx.doi.org/10.1016/j.molcatb.2014.09.0061381-1177/©2014ElsevierB.V.Allrightsreserved.24H.Kondoetal./JournalofMolecularCatalysisB:Enzymatic110(2014)23–31

Fig.1.Thereactionmechanismofl-DEXYL.l-2-haloaciddehalogenasescatalyzehydrolyticdehalogenationofl-2-haloalkanoicacidstoproducecorrespondingd-2-hydroxyalkanoicacidswithreleaseofhalideion.XandRmeanhalogenandalkylgroupincludinghydrogen,respectively.

esterintermediateandinformationonthefunctionsofactive-site